15-47919916-C-T

Position:

• chr15-47919916-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662551.1(ENSG00000259754):​n.189-72793C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 149,842 control chromosomes in the GnomAD database, including 4,284 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (4284 hom., cov: 32)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+35412C>T		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2	n.142+35412C>T		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.82+4554C>T		intron_variant, non_coding_transcript_variant
LOC124900354	XR_007064618.1	n.143-29440C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000662551.1	n.189-72793C>T		intron_variant, non_coding_transcript_variant
	ENST00000560900.1	n.195+35412C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000664705.1	n.189-72793C>T		intron_variant, non_coding_transcript_variant
	ENST00000665188.1	n.69-72793C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31445 AN: 149728 Hom.: 4281 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0871

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.210 AC: 31477 AN: 149842 Hom.: 4284 Cov.: 32 AF XY: 0.211 AC XY: 15380 AN XY: 72836

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.189

Alfa AF: 0.128 Hom.: 378

Bravo AF: 0.222

Asia WGS AF: 0.302 AC: 1044 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16960346; hg19: chr15-48212113;